ArticleBioinformatics (Oxford, England)2008
Estimating true evolutionary distances under the DCJ model.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 55 citations in OpenAlex.
- An Exact and Fast SAT Formulation for the DCJ Distance.bioRxiv : the preprint server for biology · 2024Article
- Rearrangement Events on Circular Genomes.Bulletin of mathematical biology · 2023Article
- Evolution of genome structure in theGenome research · 2021Article
- Article
- Implicit Transpositions in DCJ Scenarios.Frontiers in genetics · 2017Article
- Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation.Genome biology and evolution · 2016Article
- Moments of genome evolution by Double Cut-and-Join.BMC bioinformatics · 2015Article
- MLGO: phylogeny reconstruction and ancestral inference from gene-order data.BMC bioinformatics · 2014Article
- Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2013Article
- Phylogenetic analysis of genome rearrangements among five mammalian orders.Molecular phylogenetics and evolution · 2012Article
- UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ.Bioinformatics (Oxford, England) · 2012Article
- Bootstrapping phylogenies inferred from rearrangement data.Algorithms for molecular biology : AMB · 2012Article
- Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.BMC bioinformatics · 2011Article
- Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time.PloS one · 2011Article
- SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations.Nucleic acids research · 2010Article
- Estimating true evolutionary distances under rearrangements, duplications, and losses.BMC bioinformatics · 2010Article
- Breakpoint graphs and ancestral genome reconstructions.Genome research · 2009Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
motivationModern techniques can yield the ordering and strandedness of genes on each chromosome of a genome; such data already exists for hundreds of organisms. The evolutionary mechanisms through which the set of the genes of an organism is altered and reordered are of great interest to systematists, evolutionary biologists, comparative genomicists and biomedical researchers. Perhaps the most basic concept in this area is that of evolutionary distance between two genomes: under a given model of genomic evolution, how many events most likely took place to account for the difference between the two genomes?
resultsWe present a method to estimate the true evolutionary distance between two genomes under the 'double-cut-and-join' (DCJ) model of genome rearrangement, a model under which a single multichromosomal operation accounts for all genomic rearrangement events: inversion, transposition, translocation, block interchange and chromosomal fusion and fission. Our method relies on a simple structural characterization of a genome pair and is both analytically and computationally tractable. We provide analytical results to describe the asymptotic behavior of genomes under the DCJ model, as well as experimental results on a wide variety of genome structures to exemplify the very high accuracy (and low variance) of our estimator. Our results provide a tool for accurate phylogenetic reconstruction from multichromosomal gene rearrangement data as well as a theoretical basis for refinements of the DCJ model to account for biological constraints. AVAILABILITY: All of our software is available in source form under GPL at http://lcbb.epfl.ch.
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